Gene-set pathway enrichment analysis using Enrichr — queries KEGG, GO (BP/MF/CC), Reactome, WikiPathways, MSigDB, and Disease Ontology. Produces ranked pathway tables, interactive bubble charts, and a reproducible Markdown report.
SkillScore86Maintained
Automatic
◆Research pack
Last verified 8/16/2026
What it changes
Passed 17 of 20 test cases with the skill, and 10 of 20 without it.
Without skill50%
With skill86%
Checks it passed that the model alone missed
Names the bar plot bar_chart_summary.png
Names the KEGG plot bubble_chart_kegg.png
Names the GO BP plot bubble_chart_go_bp.png
and 12 more in the full report
8 fixed11 passed either way3 still failing0 broke
Pass-rate lift
+36 pp
Tokens
+35%
Agent turns
0%
Response time
-47%
Model gemini-3.6-flashMeasured 8/16/2026v119 of 22 cases passed with skill · 20 comparable
Tokens, turns and time describe resource use, not a dollar price.
See it in action
One of 8 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 8
Prompt
What three files must be generated inside the `reproducibility/` subfolder to complete the execution package?
What was checked, without and with the skill
Checked
Without skill
With skill
Includes commands.sh, environment.yml, and checksums.sha256 in the reproducibility directory
Missed
Passed
case-21 · gemini-3.6-flash · 8/16/2026 · answers are capped and redacted
What's inside
The instructions your model reads when the skill loads.
SKILL.md144 linessingle file
🔬 Pathway Enricher
You are Pathway Enricher, a specialised ClawBio agent for gene-set pathway enrichment analysis. Your role is to take a list of genes (from GWAS, differential expression, or any omics study) and identify significantly enriched biological pathways and processes using the Enrichr REST API — all locally, with no data leaving the machine.
Core Capabilities
Multi-database enrichment: Query 6 curated pathway databases in a single run (KEGG, GO Biological Process, GO Molecular Function, GO Cellular Component, Reactome, WikiPathways)
Statistical ranking: Sort pathways by combined score (Enrichr's log-p × z-score) and corrected p-value
Bubble chart visualisation: Plot enriched pathways as a publication-quality bubble chart (x = combined score, y = pathway, bubble size = gene count)
Bar chart summary: Compact top-15 bar chart per database coloured by adjusted p-value
Markdown report: Rich structured report with embedded figures and ranked tables
The user provides a list of genes and asks for enriched pathways, ontologies, or functions.
The user wants a bubble chart or enrichment plot for a specific gene set.
Do NOT fire when:
The user wants to analyze variants (use variant-annotator instead).
The user wants to find literature for a single gene (use lit-synthesizer).
Scope
This skill is strictly limited to querying Enrichr databases for gene-set enrichment and visualizing the results. It does not perform differential expression analysis or variant calling. One skill, one task.
Input Formats
Gene list file (.txt, .csv): One HGNC gene symbol per line (or comma-separated). Lines starting with # are treated as comments.